#rmarkdown::render(“ClusteringCoseq.Rmd”)

On cherche à construire un réseau de régulation, sur les gènes qui ont été détectés comme différentiellement exprimés lors du traitement au KNO3 des plantes WT.

Etude de la quantification

Voir les gènes non quantifiés aussi, combien, paraît beaucoup

Homogénéité des réplicats : visualisation

[1] "At_AmbientCO2_HighNitrate_Fe"

 [1] "R4"  "R5"  "R6"  "R7"  "R8"  "R9"  "R10" "R11" "R12" "R13" "R14" "R15"
[13] "R16" "R17" "R18" "R19" "R20" "R21" "R22" "R23" "R24"
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[1] "At_AmbientCO2_LowNitrate_Fe"

 [1] "R1"  "R2"  "R3"  "R7"  "R8"  "R9"  "R10" "R11" "R12" "R13" "R14" "R15"
[13] "R16" "R17" "R18" "R19" "R20" "R21" "R22" "R23" "R24"
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[1] "At_ElevatedCO2_HighNitrate_Fe"

 [1] "R1"  "R2"  "R3"  "R4"  "R5"  "R6"  "R10" "R11" "R12" "R13" "R14" "R15"
[13] "R16" "R17" "R18" "R19" "R20" "R21" "R22" "R23" "R24"
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 [ reached getOption("max.print") -- omitted 40670 entries ]
[1] "At_ElevatedCO2_LowNitrate_Fe"

 [1] "R1"  "R2"  "R3"  "R4"  "R5"  "R6"  "R7"  "R8"  "R9"  "R13" "R14" "R15"
[13] "R16" "R17" "R18" "R19" "R20" "R21" "R22" "R23" "R24"
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 [ reached getOption("max.print") -- omitted 40670 entries ]
[1] "At_AmbientCO2_HighNitrate_FeStarvation"

 [1] "R1"  "R2"  "R3"  "R4"  "R5"  "R6"  "R7"  "R8"  "R9"  "R10" "R11" "R12"
[13] "R16" "R17" "R18" "R19" "R20" "R21" "R22" "R23" "R24"
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 [ reached getOption("max.print") -- omitted 40670 entries ]
[1] "At_AmbientCO2_LowNitrate_FeStarvation"

 [1] "R1"  "R2"  "R3"  "R4"  "R5"  "R6"  "R7"  "R8"  "R9"  "R10" "R11" "R12"
[13] "R13" "R14" "R15" "R19" "R20" "R21" "R22" "R23" "R24"
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[1] "At_ElevatedCO2_HighNitrate_FeStarvation"

 [1] "R1"  "R2"  "R3"  "R4"  "R5"  "R6"  "R7"  "R8"  "R9"  "R10" "R11" "R12"
[13] "R13" "R14" "R15" "R16" "R17" "R18" "R22" "R23" "R24"
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 [ reached getOption("max.print") -- omitted 40670 entries ]
[1] "At_ElevatedCO2_LowNitrate_FeStarvation"

 [1] "R1"  "R2"  "R3"  "R4"  "R5"  "R6"  "R7"  "R8"  "R9"  "R10" "R11" "R12"
[13] "R13" "R14" "R15" "R16" "R17" "R18" "R19" "R20" "R21"
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[61]    1   51 1236    0 1928    0    0   47    0    0    0  110 1821 3420  312
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[16]    2    0    0 4119    0    0    0    0    0   27    0 3240   78    0    0
[31]    0   10    0   43    0    0  621    2 1749  117  383 1055  188 1335    0
[46]    0    9    1    0    0    0    0    0    8    6 1437    0    2    0    0
[61]    1   13  945    0 1000    0    0  117    7    0    0   59  330 1352  117
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 [1] 2083    6    0   27   22    0    4 1892    0    0    0    0    0    0    0
[16]    0    0    0 4045    0    0    0    0    0   25    0 3021   75    0    0
[31]    0   10    0   57    0    0  613    7 1520  144  410 1000  158 1516    0
[46]    0   14    1    0    0    0    0    0    9   10 1559    0    1    0    0
[61]    1   13  968    0 1085    0    0  128   11    0    0   55  364 1411  154
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 [1] 2049    0    0   39   25    0    0 1841    0    0    0    0    0    0    0
[16]    3    0    0 5493    0    0    0    0    0   28    0 4064   81    1    0
[31]    0   10    0   32    0    0  835    4  578   94  326 1229  127 1434    0
[46]    0    5    0    0    0    0    0    0    4   19 1511    0    5    0    0
[61]    0   12  869    1 1237    0    0  116    5    0    0   39  573 1588  172
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 [1] 1912    3    0   37   21    0    0 1942    0    0    0    0    0    0    0
[16]    0    0    0 5201    0    0    0    0    0   25    0 3472   88    0    0
[31]    0   11    0   45    0    0  693    2  573   90  329 1081  107 1419    0
[46]    0   11    0    0    0    0    0    0    6   20 1266    0    4    0    0
[61]    0   12  856    0 1171    0    0  128    3    0    0   28  543 1456  189
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 [1] 1542    3    0   37   21    0    1 1574    0    0    0    0    1    0    0
[16]    0    0    0 4770    0    0    0    0    0   43    0 2879   73    0    0
[31]    0   12    0   36    0    0  543    2  312   66  297 1012   76 1131    0
[46]    0   12    0    0    0    0    0    0   10   19 1373    0    0    0    0
[61]    0    8  783    1  900    0    0  116    1    0    0   37  493 1226  149
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Homogénéité des réplicats : significativité

On cherche maintenant à voir si ces plots montrent suffisamment corrélés pour montrer que les réplicats au sein d’une même condition sont suffisamment similaires. On peut déjà vérifier en plottant deux réplicats de conditions différentes : on voit que le scatter plot est plus dispersé que les réplicats biologiques.

 

A work by Océane Cassan

oceane.cassan@supagro.fr